Unfortunately, it means you put the batting upside down. Warm and white and warm and natural DO have a right side up. Oh there will be plenty here who post "I never paid any attention and never had that happen" but it does happen.
Chances are it won't wash out. You can try switching to a new, sharper needle like a top stitch or quilting needle but it may not solve your problem. You don't say if you are quilting on home machine or LA. If LA, I would recommend cutting the batting and flipping it over. But if you are quilting on a basted quilt it hardly seems worth the effort.
Google right side up on warm and natural batting and you find blogs that tell you which side is up with photos.